Most of all, how is this going to factor into Philippines' tendency for imperialism (with the 450 million taels from the ransom/indenmnity plus the fact Philippines is only one with benefiting from the silver ransom, Philippines can technically finance more colonial expansions (on military spending) if it really wishes and not get broke (money becomes less of a limit for Philippines' goals, only other factors will limit Philippines' goals (population most likely but if Philippines were to invade the Dutch and her heavily populated colonies....well, I'll just say Philippines' future is going to be interesting).
From all the spice that flow out of China, they can easily rely on Chinese mercenaries and immigrants especially from those Philippine-trained cadres and their families.I rather fear with Philippines still low population, they will be stretched thin (though if they adopt Britain's method of controlling a country by working with its leaders, that's becomes less of a problem)
I fear that Philippine's strength has gone unassailable by now compared to Japan, consigning them to a fate limited within their home islands and Hokkaido. However, that doesn't preclude them from making diplomatic agreements with those governments in Asia, however, as well as overseas who are interested in throwing Japan some bones for them to become another factor to the balance of power in the region. Those interested parties may also let Japan buy resources from them and their colonies at a bargain price, for one.I was really hoping Korea wasn't part of Treaty of Beijing hahaha... I guess I want Japan to have Korea, Northern China and be the ones to mainly deal with Russia if they ever expand while Philippines stick to the Pacific and the SEA spheres of influence (though I doubt now if Japan can pursue colonial expansion with the strategic resources more or less under Philippines spheres of influence).
However, its history will become unrecognizable anyways due to the lack of Matthew Perry's bombastic expedition, and those well-read in the Edo Period must be only be aware that the Japanese sciences and economy are, however nativised, actually on par with their European counterparts (there are only so many Japanese who can speak and read Dutch, and Western Doctors have actually demonstrated surgeries before the Shogun), so any opening up of their country will only speed up the reformist's drive for modernisation and compel the Shogun himself to give more explicit support for it. Coupled with the nativist reaction especially manifested by the Sonno Joi movement, the Komei emperor's earlier sympathetic sentiments and edicts supporting the movement, and as well as the ambition of the outsider Daimyo's especially from the Satsuma domain, it would only make for a situation ripe for political agitation, driven by the desire of centralising Japan, preferably to their own satisfaction.
If the author can't attend to much details, I'll recommend having a largely similar Bakumatsu, just with different assassinations and a different temple name for Emperor Mutsuhito. A different historiography regarding about the roles of the Tenno and the Shogun will also be appreciated.
The prospective Filipinos (those ones who chose to explore before the official diplomatic contact) being compelled to step on the Virgin Mary plates would only have engendered mistrust however. A devout Catholic, whether they be an Andresano or a Hiligaynon, reacting to that stipulation would only be interesting to see, to say the least.
The more pressing concern for this timeline, however, is China's dwindling coinage that compelled them to sell Outer Manchuria to the Russians in the 1858 Treaty of Aigun. There, the British, Russians, and Filipinos are truly at the crossroads. You can include Japan, though that's only if they're not opened because if they did, they would have been hemorrhaging gold due to Japan's difference in Gold-Silver exchange. Hence, the last one's unlikely to happen.